Combine trees and phylogenetic matrix data as a ggplot object

This function calls generate_tree_vec() to generate a vector of phylogenetic trees under parsimony. It then plots them alongside the phylogenetic matrix that was used to estimate the tree. Optional decorations can be added displaying parsimony and likelihood scores.

generate_tree_vis(sample_df, alignment, tree, phy_mat, pscore = FALSE,
  lscore = FALSE, random_tree = FALSE)

Arguments

sample_df	Dataframe specifying how to subsample phylogenetic matrix
alignment	String specifying path to alignment
tree	Starting tree for parsimony analysis. Phylo object.
phy_mat	Phylogenetic matrix to be subsampled
pscore	Optional boolean specifying if you would like figures annotated with parsimony score of tree given data. Default FALSE.
lscore	Optional boolean specifying if you would like figures annotated with likelihood score of tree given data under the Mk model. Default FALSE.
random_tree	Optional boolean specifying if you would like to view a vector of random trees

Value

vector Vector of ggplot2 objects

Examples

# NOT RUN {
output_vector <- generate_tree_vis(sample_df = sample_df,
                                   alignment = aln_path, tree = tree,
                                   phy_mat = bears, pscore = TRUE,
                                   lscore = TRUE)
# }